Selection for genetic markers in beef cattle reveals complex associations of thyroglobulin and casein1-s1 with carcass and meat traits

Effect of TG5 and LEP polymorphisms on the productivity, chemical composition, and fatty acid profile of meat from Simmental bulls

Background and Aim

Enhancing the nutritional and biological value of meat obtained from young surplus replacement animals of dual-purpose breeds is a critical objective in the livestock industry. This study aimed to investigate the impact of thyroglobulin (TG5, c. -422C > T) and leptin (LEP, c. 239C > T) polymorphisms on the productivity, chemical composition, and fatty acid (FA) profile of meat from Simmental bulls.

Materials and Methods

A total of 26 Simmental bulls were genotyped for TG5 (c. -422C > T) and LEP (c. 239C > T) polymorphisms and reared under the same fattening conditions. Controlled slaughter was conducted at 18 months of age. Subsequently, the experimental animals were evaluated to determine their slaughter traits and the chemical and FA composition of ground beef and the longissimus dorsi muscle.

Results

The results showed that the TG5 (c. -422C > T) polymorphism significantly (p < 0.05) affected the differentiation of bulls in terms of the synthesis of stearic acid, linolenic acid, and total polyunsaturated FAs, as well as the fat and dry matter content in the longissimus dorsi muscle. Conversely, the presence of the T allele in the LEP (c. 239C > T) polymorphism was associated with increased dry matter and fat in ground beef, carcass weight, and internal fat weight.

Conclusion

The analysis of slaughter traits and the chemical and FA composition of meat from the Simmental bulls genotyped for the TG5 and LEP genes revealed a genetic basis for the quantitative and qualitative characteristics of meat productivity. Thus, the genetic variability of bulls regarding the LEP and TG5 genes can be used to improve the quantitative and qualitative indicators of meat productivity in Simmental cattle through marker-assisted selection.

Production performance of cows raised with different postweaning growth patterns

The period of heifer development is a relatively small fraction of a cow's life; however, her pattern of growth may have permanent effects on her productivity as a cow. We hypothesized that altering the growth pattern during the peri-pubertal period would increase life-time productivity across genetic types of Bos taurus cows. The objective was to determine the stayability, calf production, and weight of calf weaned across six calf crops. Heifers (n = 685) were placed on one of two developmental programs at 256 ± 1 d of age. Control heifers received a diet that provided 228 kcal ME·(body weight [BW], kg) ^-0.75 daily, and stair-step heifers were allocated 157 kcal ME·(BW, kg)^-0.75 daily for 84 or 85 d, and then the daily allocation was increased to 277 kcal ME·(BW, kg)^-0.75. Stair-step heifers (0.33 ± 0.02 kg/d) had a lower average daily gain (ADG) than control heifers (0.78 ± 0.02 kg/d; P < 0.001) during Period 1, and stair-step heifers (0.93 ± 0.03 kg/d) had a greater ADG than controls (0.70 ± 0.03 kg/d; P < 0.001) during Period 2. There were no treatment (P = 0.28) or breed type differences (P = 0.42) for the proportion of cows weaning a calf; however, the proportion of cows weaning a calf decreased with cow age (P < 0.001). Calves from stair-step dams had heavier weaning weights (193 ± 1 kg) compared to control calves (191 ± 1 kg; P = 0.007). There was not a treatment (P = 0.25) or breed type differences in cumulative BW weaned (P = 0.59). A diverse genetic population of cattle within B. taurus was tested and responses in calf production did not differ between stair-step growth pattern and a more constant nonobese growth pattern.

Associations between gene polymorphisms and selected meat traits in cattle - A review

Maintaining a high level of beef consumption requires paying attention not only to quantitative traits but also to the quality and dietary properties of meat. Growing consumer demands do not leave producers many options for how animals are selected for breeding and animal keeping. Meat and carcass fatness quality traits, which are influenced by multiple genes, are economically important in beef cattle breeding programs. The recent availability of genome sequencing methods and many previously identified molecular markers offer new opportunities for animal breeding, including the use of molecular information in selection programs. Many gene polymorphisms have thus far been analyzed and evaluated as potential candidates for molecular markers of meat quality traits. Knowledge of these markers can be further applied to breeding programs through marker-assisted selection. In this literature review, we discuss the most promising and well-described candidates and their associations with selected beef production traits.

Insights into adaption and growth evolution: a comparative genomics study on two distinct cattle breeds from Northern and Southern China

Mongolian cattle (MG, Bos taurus) and Minnan cattle (MN, Bos indicus) are two different breeds of Chinese indigenous cattle, representing North type and South type, respectively. However, their value and potential have not yet been discovered at the genomic level. In this study, 26 individuals of MN and MG were sequenced for the first time at an average of 13.9- and 12.8-fold, respectively. Large numbers of different variations were identified. In addition, the analyses of phylogenetic and population structure showed that these two cattle breeds are distinct from each other, and results of linkage disequilibrium analysis revealed that these two cattle breeds have undergone various degrees of intense natural or artificial selection. Subsequently, 496 and 306 potential selected genes (PSRs) were obtained in MN and MG, containing 1,096 and 529 potential selected genes (PSGs), respectively. These PSGs, together with the analyzed copy number variation (CNV)-related genes, showed potential relations with their phenotypic characteristics, including environmental adaptability (e.g., DVL2, HSPA4, CDHR4), feed efficiency (e.g., R3HDM1, PLAG1, XKR4), and meat/milk production (e.g., PDHB, LEMD3, APOF). The results of this study help to gain new insights into the genetic characteristics of two distinct cattle breeds and will contribute to future cattle breeding.

A Review of Selected Genes with Known Effects on Performance and Health of Cattle

There are genetic conditions that influence production in dairy and beef cattle. The objective of this review was to describe relevant genetic conditions that have been associated with productivity and health in cattle. Genes or genomic regions that have been identified as a candidate for the condition will be included, and the genetic basis of the condition will be defined. Genes and genetic conditions included in this review are bovine leukocyte adhesion deficiency, deficiency of the uridine monophosphate synthase, bovine chronic interstitial nephritis, horn development, myostatin, complex vertebral malformation, leptin, osteopetrosis, apoptosis peptide activating factor 1, chondrodysplastic dwarfism, caseins, calpastatin, umbilical hernia, lactoglobulin, citrullinemia, cholesterol deficiency, prions, thyroglobulin, diacylglycerol acyltransferase, syndactyly, maple syrup urine disease, slick hair, Factor XI deficiency, and μ-Calpain. This review is not meant to be comprehensive, and relevant information is provided to ascertain genetic markers associated with the conditions.

Estimates of epistatic and pleiotropic effects of () and () genetic markers on beef heifer performance traits enhanced by selection

Genetic marker effects and type of inheritance are estimated with poor precision when minor marker allele frequencies are low. A stable composite population (MARC II) was subjected to marker assisted selection for 2 yr to equalize and genetic marker frequencies to evaluate the epistatic and pleiotropic effects of these markers on BW, reproduction, and first calf performance traits in replacement beef females ( = 171) managed under 2 postweaning development protocols. Traits evaluated on the heifers were birth BW, weaning BW, 11-mo BW, 12-mo BW, 13-mo BW, first breeding season pregnancy evaluation BW, first calving season BW, 11-mo puberty, 12-mo puberty, 13-mo puberty, first breeding season pregnancy, and first calf weaning rate. Additionally, heifer's first calf performance traits of ordinal calving date, first calf birth BW, and first calf weaning BW (with and without age adjustment) were analyzed. Selection to increase minor allele frequencies and balanced sampling across genotype classes enhanced the ability to detect all genetic effects except dominance × dominance epistasis. The × genotype effect was significant ( < 0.05) for 11-mo BW and 12-mo BW and tended to be significant ( = 0.08) for 13-mo BW. Consistently, for all 3 traits, the most significant effect among epistatic × genotype effects was the additive effect, with the G allele decreasing BW. There were no associations between × genotype and fertility related traits ( ≥ 0.46) in this study. Additionally, there were no × genotype associations with first progeny performance traits ( ≥ 0.14). The large effect of the additive × additive interaction on first calf weaning BW was imprecisely estimated, which may warrant further investigation.

A Meta-Assembly of Selection Signatures in Cattle

Since domestication, significant genetic improvement has been achieved for many traits of commercial importance in cattle, including adaptation, appearance and production. In response to such intense selection pressures, the bovine genome has undergone changes at the underlying regions of functional genetic variants, which are termed “selection signatures”. This article reviews 64 recent (2009–2015) investigations testing genomic diversity for departure from neutrality in worldwide cattle populations. In particular, we constructed a meta-assembly of 16,158 selection signatures for individual breeds and their archetype groups (European, African, Zebu and composite) from 56 genome-wide scans representing 70,743 animals of 90 pure and crossbred cattle breeds. Meta-selection-scores (MSS) were computed by combining published results at every given locus, within a sliding window span. MSS were adjusted for common samples across studies and were weighted for significance thresholds across and within studies. Published selection signatures show extensive coverage across the bovine genome, however, the meta-assembly provides a consensus profile of 263 genomic regions of which 141 were unique (113 were breed-specific) and 122 were shared across cattle archetypes. The most prominent peaks of MSS represent regions under selection across multiple populations and harboured genes of known major effects (coat color, polledness and muscle hypertrophy) and genes known to influence polygenic traits (stature, adaptation, feed efficiency, immunity, behaviour, reproduction, beef and dairy production). As the first meta-assembly of selection signatures, it offers novel insights about the hotspots of selective sweeps in the bovine genome, and this method could equally be applied to other species.

An interpretive review of selective sweep studies in Bos taurus cattle populations: identification of unique and shared selection signals across breeds

This review compiles the results of 21 genomic studies of European Bos taurus breeds and thus provides a general picture of the selection signatures in taurine cattle identified by genome-wide selection-mapping scans. By performing a comprehensive summary of the results reported in the literature, we compiled a list of 1049 selection sweeps described across 37 cattle breeds (17 beef breeds, 14 dairy breeds, and 6 dual-purpose breeds), and four different beef-vs.-dairy comparisons, which we subsequently grouped into core selective sweep (CSS) regions, defined as consecutive signals within 1 Mb of each other. We defined a total of 409 CSSs across the 29 bovine autosomes, 232 (57%) of which were associated with a single-breed (Single-breed CSSs), 134 CSSs (33%) were associated with a limited number of breeds (Two-to-Four-breed CSSs) and 39 CSSs (9%) were associated with five or more breeds (Multi-breed CSSs). For each CSS, we performed a candidate gene survey that identified 291 genes within the CSS intervals (from the total list of 5183 BioMart-extracted genes) linked to dairy and meat production, stature, and coat color traits. A complementary functional enrichment analysis of the CSS positional candidates highlighted other genes related to pathways underlying behavior, immune response, and reproductive traits. The Single-breed CSSs revealed an over-representation of genes related to dairy and beef production, this was further supported by over-representation of production-related pathway terms in these regions based on a functional enrichment analysis. Overall, this review provides a comparative map of the selection sweeps reported in European cattle breeds and presents for the first time a characterization of the selection sweeps that are found in individual breeds. Based on their uniqueness, these breed-specific signals could be considered as “divergence signals,” which may be useful in characterizing and protecting livestock genetic diversity.

Forward LASSO analysis for high-order interactions in genome-wide association study

Previous genome-wide association study (GWAS) focused on low-order interactions between pairwise single-nucleotide polymorphisms (SNPs) with significant main effects. Little is known how high-order interactions effect, especially one among the SNPs without main effects regulates quantitative traits. Within the frameworks of linear model and generalized linear model, the LASSO with coordinate descent step can be used to simultaneously analyze thousands and thousands of SNPs for normal and discrete traits. With consideration of high-order interactions among SNPs, a huge number of genetic effects make the LASSO failing to work under the presented condition of computation. Forward LASSO analysis is, therefore, proposed to shrink most of genetic effects to be zeros stage by stage. Simulation demonstrates that our proposed method could be used instead of the LASSO method for full model in mapping high-order interactions. Application of forward LASSO method is provided to GWAS for carcass traits and meat quality traits in beef cattle.